Ultimately, this leads to the conflagration of two very separate issues (and there are some who don't want to see them separated): "Where did the universe come from?" (ie- what/who is the agent of the Big Bang, et al.) and "What is the mechanism or chain of events between the Big Bang and now?" One is primarily a philosophical problem to which science can offer insight, and one is primarily a historical/scientific problem to which philosophy can offer insight. To the extent that the two can be separated, progress can be made fairly amicably. Keeping them tangled, in my opinion, is what keeps the fight so bitter.
One reason I argue for maintaining a theistically friendly worldview in science is that it keeps more possibilities open when interpreting data--let's assume for a moment that neither God nor mindless physical processes created the universe, but some third agent of whom we have not yet conceived. If your innate worldview assumes there is no supernatural, OR that the universe HAD to have been created by God, then your reading of the data is limited by that worldview. If, however, you are able to keep things a little more objective--"I don't believe in the supernatural, but I'll allow for the possibility of it in my model" and conversely, "I believe in some form of divine creation, but I'll allow for other possibilities," then you are taking the blinders off, and can let the data speak more clearly for itself.